The workflow is pretty awkward. I'm trying to replace tiles on one layer, while adding tiles to nearby layers. I sometimes end up adding tiles to the wrong layer, which is when I would like to just move them to the correct layer.

Are you saying that this isn't supported?

This is an issue because of the way the editor changes the current active layer even if you're just trying to change the visibility of a different layer by clicking the eye icon in the layer list. Changing the visibility shouldn't change the active layer. See how Gimp handles the same operation, for example.

I believe the way it works now is those tiles are forced to another layer rather then being deleted. If users could accidentally delete entire levels just by adjusting layers I think that would be a bigger problem than what you're describing here. If you want those tiles deleted then you'll have to do that before replacing them from tiles of another layer.